Split alignments are reported when one alignment contains another

[d-cameron]

For some reads, split alignments are written in which one alignment is fully contained in the other alignment using the SA tags (bwa 0.7.15).

HISEQ1:93:H2YHMBCXX:1:2214:10015:52441 2115 chrUn_JTFH01001478v1_decoy  12    1 250M    chr21   10325621       0        <snip>  NM:i:13 SA:Z:chr21,10325808,-,240M10S,9,19;

How are such split alignments to be interpreted? Can the documentation be updated to reflect the meaning of split alignments for which all bases can be aligned to one of the locations.

[d-cameron]

Duplicate of #282